Tools

Type: Experimental Tool
Project: Tolias U01

Core service provided by CSHL for in situ sequencing with BARseq on barcoded rabies virus infected brain.

Type: QC / Proofreading/ Data Validation
Project: Rivlin U01

A mesh decomposition framework for automated proofreading and morphological analysis of neuronal EM reconstructions.

Type: QC / Proofreading/ Data Validation
Project: Rivlin U01

NeuVue is a proofreading task management framework and platform for scalable curation of machine segmentation and neural circuit reconstruction from high-resolution EM connectomics data.

Type: Data Processing
Project: Fischl U01

A Python tool for multiscale nerve fiber enhancement and 3D orientation analysis in large high-resolution volumetric brain tissue reconstructions acquired by two-photon scanning or light-sheet fluorescence microscopy.

Type: Data Processing
Project: Fischl U01

A method for 3D automatic vessel segmentation across a wide range of contrasts and resolutions.

Type: Data Analysis
Project: Fischl U01

A PyTorch-based tool for automatic 3D vascular segmentation in serial-sectioning optical coherence tomography (sOCT).

Type: Data Repository
Project: Zeng U24

A data ecosystem for 3D and 4D neuroscience data, with tools and workflows for storage, access, visualization, and analysis of Electron Microscopy and X-ray Micro/Nano Tomography.

Type: Data Repository
Project: Yendiki UM1

Platform for publishing, sharing, and processing neuroscientific data.

Type: Cloud Workbench
Project: Zeng U24

A cloud platform for biomedical data analysis, secure sharing, and global collaboration. 

Type: Data Repository
Project: Pestilli U24

A cloud based platform for processing analyzing neuroscientific data via custom data workflows.

Type: Data  Processing
Project: Zeng U24

The Slide-tags Pipeline is an open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification.

Type: Data  Processing
Project: Zeng U24

The Slide-seq workflow is an open-source, cloud-optimized pipeline developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN) and the BRAIN Initiative Cell Atlas Network (BICAN). It supports the processing of spatial transcriptomic data generated with the Slide-seq (commercialized as Curio Seeker) assay.

Type: Data  Processing
Project: Zeng U24

Optimus is an open-source, cloud-optimized pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project as well as the BRAIN Initiative Cell Census Network (BICCN; see Acknowledgements below). It supports the processing of any 3' single-cell and single-nucleus count data generated with 10x Genomics assays. The following chemistries are supported:

• 10x Genomics 3' V2

• 10x Genomics 3' V3

• 10x Genomics 3' V4

• 10x Genomics 3' V4TRU

• 10x Genomics 5' V3